Tuesday, September 17, 2013

tightly patterned

For example, consider Dembski's claims about DNA. He implies that DNA has CSI [19, p. 151], but this is in contradiction to his implication that CSI can be equated with highly-compressible strings [19, p. 144]. In fact, compression of DNA is a lively research area. Despite the best efforts of researchers, only minimal compression has been achieved [36, 84, 12, 56, 2, 59].

Most highly patterned sequences have considerable redundancy, and the redundancy is often (though not always) a clue to a pattern. However, a JPEG file is hard to compress but it hardly is random. Or a more trivial example maybe, a Zip file is hard to compress but is certainly not random. These are tightly patterned. We do not know how tightly patterned portions of DNA are because we don't know how much of it works. The most well understood part of DNA -- what specifies protein structure -- has a lot of redundancy built into it. Many of the codons that make up protein DNA can be compressed to 4 or 5 bits if we knew for a fact that they were only being used to specify one protein, i.e. they only had one specificational role in one gene. But that isn't necessarily true, meaning that many genes are more tightly patterned than can be ascertained at first glance. For those that aren't, codons that can be replaced with a codon for a more or less equivalent amino acid often are. This replaces one kind of redundancy (one that with less variation might allow more compression of a genome) with another (one that increases the Shannon entropy of the genome).

We know so little, despite the amazing things that have been learned, about the language of development. Ironically, even if the neo-Darwinian paradigm were true, it gives so little information about what to expect that it actually works against understanding. Biologists going in expect things to be put together in an incoherent way. They have a nearly behaviorist model of the DNA code and do not approach it as a coherent program, even as they more or less describe it as a coherent program that arose through an incoherent process. It must be hopelessly cobbled together because the Modern Synthesis tells us that it was hopelessly cobbled together.

One study suggest a lot of internal structure to the genome, making one wonder just how tightly patterned it is.